Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ctf1

Cell type

Cell type Class
Neural
Cell type
Cerebral Cortex
MeSH Description
Type of cerebral cortex which does not pass through a perinatal phase of six-layered structure as in the NEOCORTEX and develops into three or four layers in the mature brain. Allocortex has three subareas: archi- paleo- and periallo-cortex.

Attributes by original data submitter

Sample

source_name
cerebral cortex
experiment
TranscriptionFactorChIPseq
age
E12.5
tissue
Cortex
chip antibody
CTF1
replicate
Rep3
genotype
WT

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclear extracts were prepared from sorted cells and digested with MNase to obtain mono- and di-nucleotide fragments. Digested chromatin was dialysed overnight. Input control chromatin was set aside, and immunoprecipitation reactions were performed with antibodies against H3K27ac (Abcam, ab472) or H3K27me3 (Active motif, 39157). Precipitated fractions were purified using Dynabeads (Invitrogen) and RNase-treated prior to library construction. Libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen), size selected in the range of 180-300 bp on a BluePippin (Sage Science), quality control tested on a Bioanalyzer (Agilent) and sequenced on a HiSeq 4000 (Illumina). Nuclear extracts were prepared from cells and sheared using a bioruptor (18-40 cylces; 30s ON and 45s OFF). Input control chromatin was set aside, and immunoprecipitation reactions were performed with antibodies against the relevant TF or IgG or a blocking peptide overnight at 4C. Precipitated fractions were purified using Dynabeads (Invitrogen) and RNase-treated prior to library construction. Libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen), size selected in the range of 180-300 bp on a BluePippin (Sage Science), quality control tested on a Bioanalyzer (Agilent) and sequenced on a HiSeq 4000 (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
43919045
Reads aligned (%)
97.5
Duplicates removed (%)
29.5
Number of peaks
1017 (qval < 1E-05)

mm9

Number of total reads
43919045
Reads aligned (%)
97.3
Duplicates removed (%)
29.6
Number of peaks
1064 (qval < 1E-05)

Base call quality data from DBCLS SRA